Hi Christoph, I tried increasing the box length in z direction, but the error still persists. Its two layers of graphene each have 96 atoms.
The errors is: "I have 192 beads in 2 molecules I have 48 beads in 2 molecules for the coarse graining Reading frame 0 time 0.000 *1.1281.5872.668 0.3381.1411.688* an error occurred: coarse-grained bead is bigger than half the box (atoms C (id 1), C (id 21) , molecule 1)" Is there an issue with the atomistic simulation? On Sat, Jan 16, 2021 at 7:44 PM Christoph Junghans <[email protected]> wrote: > On Sat, Jan 16, 2021 at 1:40 AM Pragati Sharma <[email protected]> > wrote: > > > > Dear all, > > > > Can the coarse grain potentials using IBI for graphene sheet which is > periodic along xy direction be performed in votca. > > > > I am trying to do it and it's throwing an error saying the "bead is > bigger than half of the box". > This check is in there to avoid non-unique mapping of the position in > case of periodic boundary conditions. > You could certainly modify the code to disable it and see what > happens, but my guess is your setup of the sheet has a very small box > length in z. > As that is mainly empty space, just try to increase the box size by a > factor 10 in z or so. > > Above the error message VOTCA prints out two vectors, the first 3 > numbers are the position of the reference point for the pbc > calculations r0 and the next 3 numbers are the positions of the atoms > that are too far away from r0. Can you post these numbers? > > Christoph > > > Any ideas on this. > > > > Thanks > > > > -- > > Join us on Slack: https://join.slack.com/t/votca/signup > > --- > > You received this message because you are subscribed to the Google > Groups "votca" group. > > To unsubscribe from this group and stop receiving emails from it, send > an email to [email protected]. > > To view this discussion on the web visit > https://groups.google.com/d/msgid/votca/CAMpF9Q3hL857_shxbt-bCSZ7Kf6vrbkGt%3D1DFVUE1CBYSd7qCA%40mail.gmail.com > . > > > > -- > Christoph Junghans > Web: http://www.compphys.de > > -- > Join us on Slack: https://join.slack.com/t/votca/signup > --- > You received this message because you are subscribed to the Google Groups > "votca" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to [email protected]. > To view this discussion on the web visit > https://groups.google.com/d/msgid/votca/CAHG27e5Gy7wZSdt6ALR9r4gWb79vf8nzeGX0ZrzbSwgFBXZvtQ%40mail.gmail.com > . > -- Join us on Slack: https://join.slack.com/t/votca/signup --- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To view this discussion on the web visit https://groups.google.com/d/msgid/votca/CAMpF9Q3rBGmNYzPpiv7eH6MQJ2Zkwqr1BzDTAC0HoqXXOT_bow%40mail.gmail.com.
